Post-polymerase Chain Reaction Research Articles

Evaluation of Post-Polymerase Chain Reaction Melting Temperature Analysis for Meat Species Identification in Mixed DNA Samples

Real-time uniplex and duplex polymerase chain reaction (PCR) assays with a SYBR Green I post-PCR melting curve analysis were evaluated for the identification and quantification of bovine, porcine, horse, and wallaroo DNA in food products. Quantitative values were derived from threshold-cycle (C(t)) data obtained from serial dilutions of purified DNA. The limits of detection in uniplex reactions were 0.04 pg for porcine and wallaroo DNA and 0.4 pg for cattle and horse DNA. Species specificity of the PCR products was tested by the identification of peaks in DNA melting curves, measured as the decrease of SYBR Green I fluorescence at the dissociation temperature. The peaks could be distinguished above the background even at the lowest amount of template DNA detected by the C(t) method. The system was also tested in duplex reactions, by use of either single-species DNA or DNA admixtures containing different shares of two species. The minimum proportions of each DNA species allowing the resolution of T(m) peaks in the duplex reactions were 5% (cattle or wallaroo) in cattle/wallaroo mixtures, 5% porcine and 1% horse in porcine/horse mixtures, 60% porcine and 1% wallaroo in porcine/wallaroo mixtures, and 1% cattle and 5% horse in cattle/horse mixtures. A loss in the sensitivity of the method was observed for some DNA combinations in the duplex assay. In contrast, the results obtained from SYBR Green I uniplex and duplex reactions with single-species DNA were largely comparable to those obtained previously with species-specific TaqMan probes, showing the suitability of that simpler experimental approach for large-scale analytical applications.

DIAGNOSING INFECTION LEVELS OF FOUR HUMAN MALARIA PARASITE SPECIES BY A POLYMERASE CHAIN REACTION/LIGASE DETECTION REACTION FLUORESCENT MICROSPHERE-BASED ASSAY

Improving strategies for diagnosing infection by the four human Plasmodium species parasites is important as field-based epidemiologic and clinical studies focused on malaria become more ambitious. Expectations for malaria diagnostic assays include rapid processing with minimal expertise, very high specificity and sensitivity, and quantitative evaluation of parasitemia to be delivered at a very low cost. Toward fulfilling many of these expectations, we have developed a post-polymerase chain reaction (PCR)/ligase detection reaction-fluorescent microsphere assay (LDR-FMA). This assay, which uses Luminex FlexMAP microspheres, provides simultaneous, semi-quantitative detection of infection by all four human malaria parasite species at a sensitivity and specificity equal to other PCR-based assays. In blinded studies using P. falciparum-infected blood from in vitro cultures, we identified infected and uninfected samples with 100% concordance. Additionally, in analyses of P. falciparum in vitro cultures and P. vivax-infected monkeys, comparisons between parasitemia and LDR-FMA signal intensity showed very strong positive correlations (r > 0.95). Application of this multiplex Plasmodium species LDR-FMA diagnostic assay will increase the speed, accuracy, and reliability of diagnosing human Plasmodium species infections in epidemiologic studies of complex malaria-endemic settings.

Sequence-specific Priming and Exonuclease-released Fluorescence Assay for Rapid and Reliable HLA-A Molecular Typing.

Background: The rapid and sensitive method described for low-resolution DNA typing of alleles at the HLA-A locus is based on a sequence-specific primer polymerase chain reaction approach that eliminates post-polymerase chain reaction gel electrophoresis to analyze the results. Methods and Results: This method takes advantage of the 5' --> 3' exonuclease activity of the Taq polymerase normally present during polymerase chain reaction. This sequence-specific priming and exonuclease-released fluorescence assay was conducted on 40 DNA samples derived from homozygous cell lines and peripheral blood lymphocytes that represented the majority of the HLA-A alleles. There was 100% condordance with the results obtained by serologic typing of these same samples. Conclusions: The advantages of this system are that assays can be performed in 2 hours, the results are easy to interpret, and no gel electrophoresis is required. The same strategy can be used for high-resolution DNA typing once appropriate primer pairs are added to the panel used for first-level discrimination.

The detection of lumpy skin disease virus in samples of experimentally infected cattle using different diagnostic techniques

Lumpy skin disease (LSD) is a disease of cattle, primarily in Africa and Madagascar and rarely in the Middle East. It is caused by a capripoxvirus that belongs to the family Poxviridae. The disease is of economic importance in endemic areas. Effective control of LSD requires accurate and rapid laboratory techniques to confirm a tentative clinical diagnosis. Comparative studies on different diagnostic tests used at different stages of the disease have not been done. The aim of this study was to compare several of these tests. Six seronegative bulls, between 11 and 20 months of age, were infected intravenously and kept in an insect-free facility. The course of the infection was monitored. During a 3-month period blood samples and skin biopsies were collected for virus isolation and polymerase chain reaction (PCR). Skin biopsies were also examined using transmission electron microscopy (TEM). The incubation period in infected animals varied from 4-5 days. The length of the viraemic period did not correlate with the severity of clinical disease. Viraemia was detected from 1-12 days using virus isolation and from 4-11 days using the PCR, which is longer than has previously been reported. Virus was isolated from skin biopsies until Day 39 post infection (p.i.) and PCR could demonstrate viral DNA until Day 92 p.i. Transmission electron microscopy of negatively stained skin biopsies detected LSD virus only in one of the four bulls that developed skin lesions until Day 33 p.i. The PCR was a fast and sensitive method to demonstrate viral DNA in blood and skin samples. It could detect viral nucleic acid in skin lesions 53 days longer than virus isolation. Virus isolation from blood and skin samples was sensitive and reliable, but as a single test it may be too time-consuming to use although this depends on how rapidly the diagnosis must be confirmed. In conclusion, this study showed the PCR to be superior in detecting LSD virus from blood and skin samples. However, virus isolation is still required when the infectivity of the LSD virus is to be determined.

A prospective randomized study to compare the molecular response rates between central lymphatic irradiation (CLI) and intensive alternating triple chemotherapy (ATT) in the treatment of stage I-III follicular lymphoma

A prospective randomized study to compare the molecular response rates between central lymphatic irradiation (CLI) and intensive alternating triple chemotherapy (ATT) in the treatment of stage I-III follicular lymphoma

Direct identification of all oncogenic mutants in KRAS exon 1 by cycling temperature capillary electrophoresis.

Over the past few decades, advances in genetics and molecular biology have revolutionized our understanding of cancer initiation and progression. Molecular progression models outlining genetic events have been developed for many solid tumors, including colon cancer. Previous reports in the literature have shown a relationship between different KRAS mutations and prognosis and response to medical treatment in colon cancer patients. Furthermore, the presence of a mutated KRAS has been correlated with different clinicopathological variables including age and gender of patients and tumor location. To our knowledge, few institutions screen for KRAS mutations on regular basis in colon cancer patients despite such evidence that knowledge of KRAS exon 1 status is informative. Here, we report on a mutation analysis method adapted to a 96-capillary electrophoresis instrument that allows identification of all 12 oncogenic mutations in KRAS exon 1 under denaturing conditions. To determine the optimal parameters, a series of DNA constructs generated by site-directed mutagenesis was analyzed and the migration times of all mutant peaks were measured. A classification tree was then made based on the differences in migration time between the mutants and an internal standard. A randomized series of 500 samples constructed with mutagenesis as well as 60 blind samples from sporadic colon carcinomas was analyzed to test the method. No wild-type samples were scored as mutants and all mutants were correctly identified. Post polymerase chain reaction (PCR) analysis time of 96 samples was performed within 40 min.

SNP genotyping by the 5'-nuclease reaction.

The chief attribute of the fluorogenic 5′ nuclease assay is that it is completely homogeneous. After mixing the sample and reaction components, the assay is run in a closed tube format with no postpolymerase chain reaction (PCR) processing steps. Results are obtained by simply measuring the fluorescence of the completed reactions. By eliminating post-PCR processing, allelic discrimination with fluorogenic probes reduces the time of analysis, eliminates the labor and supply costs of post-PCR steps, reduces the risk of crossover contamination, and minimizes sources of error. The assay has the sensitivity of PCR so that a minimum amount of genomic DNA is required. The use of endpoint fluorescence measurements maximizes throughput. Using a single ABI Prism® 7900HT Sequence Detection System and 24-h operation, it is possible to generate up to 250,000 SNP results per day. TaqMan® MGB probes and the entire operating system outlined below make it possible to quickly apply the 5′ nuclease assay to any allelic discrimination application where high throughput is of paramount concern.

Genotyping of human platelet antigen-1 by gene amplification and labelling in one system and automated fluorescence correlation spectroscopy.

Genotyping of human platelet antigen-1 (HPA-1) is required for the diagnosis and appropriate therapy of alloimmunization. Recently, the HPA-1 polymorphism has been identified as an inherited risk factor for thrombosis. Most currently used methods for HPA-1 genotyping have the disadvantage of time-consuming post-polymerase chain reaction (PCR) processes such as ligation (oligonucleotide ligation assay), restriction enzyme digestion (allele-specific restriction enzyme analysis) and electrophoresis (single-strand conformation polymorphism). We present a novel method for HPA-1 genotyping based on a homogeneous PCR strategy (GALIOS, gene amplification and labelling in one system) combined with automated fluorescence correlation spectroscopy (FCS). The PCR uses one pair of gene-specific amplification primers and two allele-specific, semi-nested labelling primers. The allele-specific labelling primers differ in a single nucleotide (T for HPA-1a/1a, C for HPA-1b/1b) and are coupled to different fluorescent dyes. The quantities of generated fluorescent PCR products are analysed by FCS at 543 nm and 633 nm excitation wavelength respectively. The genotypes determined using this method were in 100% concordance with the results obtained by allele-specific restriction analysis (n = 380 samples). The assay was validated for specificity, reliability and the dynamic range. This innovative method of rapid HPA-1 genotyping offers a specific and robust system, which is applicable for routine HPA-1 genotyping.

Linear dichroism for the detection of single base pair mutations.

Flow linear dichroism is shown to be able to detect single base mismatches in a polymerase chain reaction (PCR) amplimers from exon 10 of the human beta-glucocerebrosidase gene (associated with Gaucher disease) over a kilobase long with no post PCR manipulation.

Impact of Ultra-Sensitive technology and contemporary therapy on laboratory results.

The introduction of ultra-sensitive labels for immunoassays has exposed some of the limitations inherent in them. Thus, for instance a major problem with acridinium esters used, as chemiluminescence label is the formation of the so called "pseudobases" at an alkaline pH, which if not suppressed can affect the rate of the chemiluminescence reaction. Chemiluminescence labels such as luminol can also be problematic when attached to antibodies and small molecules to the extent that the sensitivity of the assay can be reduced by the decrease in the intensity of chemiluminescence. The increased use of molecular methods such as polymerase chain reaction (PCR) and post PCR methods to study mutations have various pittalls, which if unrecognized and uncontrolled can lead to incorrect results and misinterpretation. Patients who are exposed to mouse immunoglobulins through imaging or therapeutic techniques can develop antibodies to mouse immunoglobulins (human anti-mouse antibodies or HAMA) which can be a major problem for non optimized immunoassays using murine monoclonal antibodies. The types of therapy such as anticoagulant used in anticoagulant therapy, blood substitute and drug therapy can impact on the measurements of some of the biochemical and other analytes. One must separate the transient, physiological effects introduced by therapy from long-term biochemical alterations due to disease.

Rapid method for relative gene expression determination in human tissues using automated capillary gel electrophoresis and multicolor detection

The aim of this study was to evaluate a direct and automated post-polymerase chain reaction (PCR) detection system to simultaneously determine the relative gene expression levels of nine cancer-related human genes. Total RNA was prepared from flash-frozen biopsies derived from human colorectal tumors or normal mucosa and reverse-transcribed to cDNA which was PCR-amplified using primer pairs corresponding to the studied genes. In each reaction, the forward primer was labeled with a fluorescent dye. The PCR products were pooled and an internal size standard with a uniquely colored fluorescent dye was added. The samples were then subjected to automated capillary gel electrophoresis. Fragment analysis software was used to calculate the relative gene expression using β-actin as the reference gene. We found that automated capillary gel electrophoresis with multicolor detection is a rapid, accurate and highly reproducible method for separation and quantification of PCR-amplified cDNA.

Detection of adenovirus using PCR and molecular beacon

The polymerase chain reaction (PCR) and a molecular beacon probe were used for the detection of Adenovirus. A 307 bp DNA fragment from a conserved region of the hexon gene was amplified. The specific molecular beacon was characterized with respect to its efficiency of quenching, and signal to noise ratio by spectrofluorometric analysis of its hybridization with virus specfic complementary single stranded oligonucleotide target. Amplification was carried out in the presence of the molecular beacon probe, and the amplified target was detected by measurement of fluorescence signal in the post PCR sample. Separately, a 32P-labeled linear probe (having the same sequence as that of molecular beacon probe) was liquid-phase hybridized with the product of PCR performed in the absence of the molecular beacon. The virus specific target was then detected by electrophoresis of the hybridized product in a nondenaturing polyacrylamide gel and subsequent autoradiographic analysis. The detection limit of adenovirus by PCR in the presence of the molecular beacon probe was found to be similar to that obtained by labeled linear probe hybridization following PCR.

Solid-phase sequence scanning for drug resistance detection in tuberculosis

DNA chip arrays hold considerable promise for diagnostic sequencing of polymerase chain reaction (PCR) products. To date, however, arrays have been relatively expensive, complex to use and difficult to interpret, preventing their adaptation to the clinical lab. A moderate density array method has been developed that enables efficient, easy-to-interpret and robust solid-phase PCR product sequencing. Here, the results ofMycobacterium tuberculosisrifampin resistance mutation detection by primer-extension-based sequence scanning of therpoB gene ofM. tuberculosisare presented. Rifampin resistant clinical isolates were identified in as little as 1 h post PCR amplification with visual results detection.

Detection of the Hereditary Hemochromatosis Gene Mutation by Real-Time Fluorescence Polymerase Chain Reaction and Peptide Nucleic Acid Clamping

Hereditary hemochromatosis (HH), an iron overload disease, is the most common known inheritable disease. The most prevalent form of HH is believed to be the result of a single base-pair mutation. We describe a rapid homogeneous mutation analysis method that does not require post-polymerase chain reaction (PCR) manipulations. This method is a marriage of three emerging technologies: rapid cycling PCR thermal cyclers, peptide nucleic acid (PNA) probes, and a new double-stranded DNA-selective fluorescent dye, Sybr Green I. The LightCycler is a rapid thermal cycler that fluorometrically monitors real-time formation of amplicon with Sybr Green I. PNAs are DNA mimics that are more sensitive to mismatches than DNA probes, and will not serve as primers for DNA polymerases. PNA probes were designed to compete with PCR primers hybridizing to the HH mutation site. Fully complemented PNA probes at an 18:1 ratio over DNA primers with a mismatch result in suppression of amplicon formation. Conversely, PNA probes with a mismatch will not impair the binding of a complementary primer, culminating in amplicon formation. A LightCycler-based rapid genetic assay has been developed to distinguish HH patients from HH carriers and normal individuals using PNA clamping technology.

Application of Capillary Electrophoresis to the Post-Polymerase Chain Reaction Analysis of Rat mRNA for Gastric H+,K+-ATPase

We have developed a competitive quantitative RNA/polymerase chain reaction (PCR) method using capillary electrophoresis in the post-PCR analysis for the quantitation of rat gastric H+,K+-ATPase mRNA. Analysis with CE allows quick and direct separation, evaluation, and characterization of DNA fragments similar in size, and it offers a convenient way of automatizing the post-PCR analysis. To estimate the magnitudes of different error contributions affecting the accuracy and reproducibility of the results, an analysis of variance was performed using the data obtained from quantitating mRNA levels in 10 different total RNA extracts from the Corpus region of Sprague-Dawley rats. The result showed that the reproducibility of the method of analysis was sufficient for the determination of H+,K+-ATPase mRNA levels among animals even when small fluctuations in RNA synthesis are to be measured. A comparison was also made of the mRNA levels of the β- and α- subunits of H+,K+-ATPase, and the results were found to be in the same level.